I designed this This 3D printed case for the chocV keyboard as I didn't want to carry a bare PCB in my backpack. Tried to keep it as lowpro as possible by using Peel-a-way sockets to socket the MCU.
You'll probably have to experiment with 4/5mm standoffs to see which one works best for you to mount the PCB to the case, and the MCU cover to the PCB.
For any other questions, please contact me via Discord@ sato40